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- PDB-6gw7: The CTD of HpDprA, a DNA binding Winged Helix domain which do not... -

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Basic information

Entry
Database: PDB / ID: 6gw7
TitleThe CTD of HpDprA, a DNA binding Winged Helix domain which do not bind dsDNA
ComponentsDNA protecting protein DprA
KeywordsDNA BINDING PROTEIN / Winged Helix / DprA / Helicobacter pylori
Function / homologyDNA recombination-mediator protein A / DNA recombination-mediator protein A / DNA-mediated transformation / DNA protecting protein DprA
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsLisboa, J. / Celma, L. / Sanchez, D. / Marquis, M. / Andreani, J. / Guerois, R. / Ochsenbein, F. / Durand, D. / Marsin, S. / Cuniasse, P. ...Lisboa, J. / Celma, L. / Sanchez, D. / Marquis, M. / Andreani, J. / Guerois, R. / Ochsenbein, F. / Durand, D. / Marsin, S. / Cuniasse, P. / Radicella, J.P. / Quevillon-Cheruel, S.
Funding support France, 3items
OrganizationGrant numberCountry
French National Research AgencyANR-10-INSB-05-01 France
French National Research AgencyANR-IAB-2011 France
French National Research AgencyANR-10-BLAN-1328 France
CitationJournal: Febs J. / Year: 2019
Title: The C-terminal domain of HpDprA is a DNA-binding winged helix domain that does not bind double-stranded DNA.
Authors: Lisboa, J. / Celma, L. / Sanchez, D. / Marquis, M. / Andreani, J. / Guerois, R. / Ochsenbein, F. / Durand, D. / Marsin, S. / Cuniasse, P. / Radicella, J.P. / Quevillon-Cheruel, S.
History
DepositionJun 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2May 29, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 18, 2020Group: Data collection / Refinement description / Category: pdbx_nmr_spectrometer / refine / Item: _pdbx_nmr_spectrometer.model
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA protecting protein DprA


Theoretical massNumber of molelcules
Total (without water)7,1391
Polymers7,1391
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5250 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80structures with the least restraint violations
RepresentativeModel #7fewest violations

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Components

#1: Protein DNA protecting protein DprA


Mass: 7139.292 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: BB415_01075
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A2A6XLY0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-13C NOESY aliphatic
121isotropic13D 1H-13C NOESY aromatic
131isotropic13D 1H-15N NOESY
343isotropic22D 1H-15N HSQC
151isotropic23D 1H-15N TOCSY
161isotropic23D HNCA
171isotropic23D HBHA(CO)NH
181isotropic23D CBCA(CO)NH

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1128 uM 15N,13C HpDprA CTD, 90% H2O/10% D2O15N13C_sample_H2O90% H2O/10% D2O
solution2128 uM [U-13C; U-15N] C-terminal Domain of Helicobacter Pylori RecA-loader DNA Processing Protein A (DprA), 100% D2O15N13C_sample_D2O100% D2O
solution334 uM [U-15N] C-terminal Domain of Helicobacter Pylori RecA-loader DNA Processing Protein A (DprA), 90% H2O/10% D2O15N_sample_H2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
128 uMHpDprA CTD15N,13C1
128 uMC-terminal Domain of Helicobacter Pylori RecA-loader DNA Processing Protein A (DprA)[U-13C; U-15N]2
34 uMC-terminal Domain of Helicobacter Pylori RecA-loader DNA Processing Protein A (DprA)[U-15N]3
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
1138 uM 20 mM phosphate buffer (NH2PO4), NaCl 50 mM, 0.1 mM EDTA, 0.1 mM DSS, 0.1 mM NaN3, protease inhibitors (Roche)50 mM15N13C_sample_H2O5.6 1 atm298 K
220 mM phosphate buffer (NH2PO4), NaCl 50 mM, 0.1 mM EDTA, 0.1 mM DSS, 0.1 mM NaN3, protease inhibitors (Roche)50 mM13C15N_sample_D2O5.6 pD1 atm298 K
334 uM HpDprA CTD sample Tris Buffer NaCl50 mM15N_sample_titration7.4 1 atm300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9501
Bruker DRXBrukerDRX6002

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.24data extraction
NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
SparkyGoddardchemical shift assignment
CcpNmr AnalysisCCPNdata analysis
CANDIDHerrmann, Guntert and Wuthrichstructure calculation
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 80 / Conformers submitted total number: 20

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